[Vegan-commits] r390 - in branches/1.13: R data inst man

[noreply at r-forge.r-project.org]

Author: jarioksa
Date: 2008-06-04 08:45:21 +0200 (Wed, 04 Jun 2008)
New Revision: 390

Added:
   branches/1.13/data/mite.xy.rda
Modified:
   branches/1.13/R/taxa2dist.R
   branches/1.13/inst/ChangeLog
   branches/1.13/man/mite.Rd
Log:
merged r368 (taxa2dist method name) and r371 (mite.xy) from pkg/ branches/1.13

Modified: branches/1.13/R/taxa2dist.R
===================================================================
--- branches/1.13/R/taxa2dist.R	2008-06-03 20:03:00 UTC (rev 389)
+++ branches/1.13/R/taxa2dist.R	2008-06-04 06:45:21 UTC (rev 390)
@@ -28,6 +28,7 @@
         out <- out + add[i + 1] * outer(x[, i], x[, i], "!=")
     }
     out <- as.dist(out)
+    attr(out, "method") <- "taxa2dist"
     attr(out, "steps") <- add
     if (missing(labels)) {
         attr(out, "Labels") <- rownames(x)

Copied: branches/1.13/data/mite.xy.rda (from rev 389, pkg/data/mite.xy.rda)
===================================================================
(Binary files differ)

Modified: branches/1.13/inst/ChangeLog
===================================================================
--- branches/1.13/inst/ChangeLog	2008-06-03 20:03:00 UTC (rev 389)
+++ branches/1.13/inst/ChangeLog	2008-06-04 06:45:21 UTC (rev 390)
@@ -1,3 +1,4 @@
+
 $Date$
 
 VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/
@@ -4,6 +5,10 @@
 
 Version 1.13-1 (opened May 22, 2008)
 
+	* merged 371: mite.xy data.
+
+	* merged 368: method name to taxa2dist
+	
 	* merged r365: workaround to failure of weights.default in R 2.7.0
 	when object had no weights.
 

Modified: branches/1.13/man/mite.Rd
===================================================================
--- branches/1.13/man/mite.Rd	2008-06-03 20:03:00 UTC (rev 389)
+++ branches/1.13/man/mite.Rd	2008-06-04 06:45:21 UTC (rev 390)
@@ -2,6 +2,7 @@
 \alias{mite}
 \alias{mite.env}
 \alias{mite.pcnm}
+\alias{mite.xy}
 \docType{data}
 \title{Oribatid Mite Data with Explanatory Variables
   }
@@ -13,11 +14,13 @@
 data(mite)
 data(mite.env)
 data(mite.pcnm)
+data(mite.xy)
 }
 \format{
   There are three linked data sets: \code{mite} that contains the data
   on 35 species of Oribatid mites, \code{mite.env} that contains
-  environmental data in the same sampling sites, and \code{mite.pcnm}
+  environmental data in the same sampling sites, \code{mite.xy}
+  that contains geographic coordinates,  and \code{mite.pcnm}
   that contains 22 PCNM base functions (columns) computed from the geographic
   coordinates of the 70 sampling sites (Borcard & Legendre 2002).
   The whole sampling area was 2.5 m x 10 m in size.